get_snp_matrices: Get SNP data matrices from VCF object(s)

In single-cell-genetics/cardelino: Clone Identification from Single Cell Data

Get SNP data matrices from VCF object(s)

Description

Get SNP data matrices from VCF object(s)

Usage

get_snp_matrices(vcf_cell, vcf_donor = NULL, verbose = TRUE, donors = NULL)

Arguments

vcf_cell	a CollapsedVCF object containing variant data for cells
vcf_donor	an optional CollapsedVCF object containing genotype data for donors
verbose	logical(1), should the function output verbose information as it runs?
donors	optional character vector providing a set of donors to use, by subsetting the donors present in the donor_vcf_file; if NULL (default) then all donors present in VCF will be used.

Value

a list containing A, a matrix of integers. Number of alteration reads in SNP i cell j. D, a matrix of integers. Number of reads depth in SNP i cell j. R, a matrix of integers. Number of reference reads in SNP i cell j. GT_cells, a matrix of integers for genotypes. The cell-SNP configuration. GT_donors, a matrix of integers for genotypes. The donor-SNP configuration.

Examples

vcf_cell <- read_vcf(system.file("extdata", "cells.donorid.vcf.gz",
                     package = "cardelino"))
vcf_donor <-  read_vcf(system.file("extdata", "donors.donorid.vcf.gz",
                       package = "cardelino"))
snp_data <- get_snp_matrices(vcf_cell, vcf_donor)

single-cell-genetics/cardelino documentation built on Nov. 22, 2022, 4:05 p.m.